Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 54095.35 
• Atom Count: 3625 
• Residue Count: 470 
• Unique protein chains: 1

3ID8

Ternary complex of human pancreatic glucokinase crystallized with activator, glucose and AMP-PNP

• DOI: 10.2210/pdb3ID8/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2009-07-20 Released: 2010-07-28 
• Deposition Author(s): Petit, P., Gluais, L., Lagarde, A., Boutin, J.A., Ferry, G., Vuillard, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.279 
• R-Value Work: 0.201 

Literature

The active conformation of human glucokinase is not altered by allosteric activators

Petit, P., Antoine, M., Ferry, G., Boutin, J.A., Lagarde, A., Gluais, L., Vincentelli, R., Vuillard, L.

(2011) Acta Crystallogr.,Sect.D 67: 929-935

• PubMed: 22101819 
• DOI: 10.1107/S0907444911036729
• Primary Citation of Related Structures:  
  4NO7, 3IDH, 3FGU, 3F9M


• PubMed Abstract: 
  

Glucokinase (GK) catalyses the formation of glucose 6-phosphate from glucose and ATP. A specific feature of GK amongst hexokinases is that it can cycle between active and inactive conformations as a function of glucose concentration, resulting in a unique positive kinetic cooperativity with glucose, which turns GK into a unique key sensor of glucose metabolism, notably in the pancreas. GK is a target of antidiabetic drugs aimed at the activation of GK activity, leading to insulin secretion. Here, the first structures of a GK-glucose complex without activator, of GK-glucose-AMP-PNP and of GK-glucose-AMP-PNP with a bound activator are reported. All these structures are extremely similar, thus demonstrating that binding of GK activators does not result in conformational changes of the active protein but in stabilization of the active form of GK.

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Organizational Affiliation: 

BioXtal, PX Unit, c/o AFMB, UMR 6098, Case 932, 163 Avenue de Luminy, 13288 Marseille CEDEX 09, France.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Glucokinase	A	470	Homo sapiens	Mutation(s): 0  Gene Names: GCK EC: 2.7.1.2
Find proteins for P35557 (Homo sapiens) Go to Gene View: GCK Go to UniProtKB:  P35557

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
K	A	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
MRK	A	2-AMINO-4-FLUORO-5-[(1-METHYL-1H-IMIDAZOL-2-YL)SULFANYL]-N-(1,3-THIAZOL-2-YL)BENZAMIDE C14 H12 F N5 O S2 YUCYMQBDBXVNCE-UHFFFAOYSA-N
ANP	A	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
GLC	A	ALPHA-D-GLUCOSE C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
MRK	EC50: 67.1 nM (99) BINDINGDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.279 
• R-Value Work: 0.201 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 67.000	α = 90.00
b = 82.600	β = 90.00
c = 86.800	γ = 90.00

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
XSCALE	data scaling
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-07-20 
• Released Date: 2010-07-28 
• Deposition Author(s): Petit, P., Gluais, L., Lagarde, A., Boutin, J.A., Ferry, G., Vuillard, L.

Revision History 

• Version 1.0: 2010-07-28
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance
• Version 1.2: 2011-11-09
  Type: Database references
• Version 1.3: 2012-04-25
  Type: Database references